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CommanderSisko and MajorKira Nerys are in dispute over a Valerianfreighter that is requesting permission to dock at the station. Kira wants to deny their request because the Valerians ran weapons-grade dolamide to the Cardassians during the Occupation of Bajor, and she believes that they are still continuing to do so. Sisko asserts that without proof, there is nothing that they can do. He appeases Kira by promising to contact the Federation about the matter if she brings him solid proof. In the meantime, the Valerians will be allowed to dock.

A KlingonVor'cha-classattack cruiser, the IKS Toh'Kaht, returns from an expedition through the wormhole a month ahead of schedule. Immediately after clearing the event horizon, the vessel explodes. A Klingon officer, Hon'Tihl, barely manages to materialize on the transporter pad, but the transport does not stabilize properly. O'Brien and Dax launch into action and coordinate the sensors allowing Hon'Tihl to fully materialize, but he immediately collapses. DoctorBashir rushes over to tend to him, and as he leans over, Hon'Tihl grins and hisses the word "Victory!" before dying.

"Station log, stardate 46922.3. We have identified the dead Klingon. His name was Hon-Tihl, First Officer of the Toh'Kaht. Why he died, and the cause of his ship's destruction, is still unknown."

Bashir tells Kira, Sisko, O'Brien, and Odo that he found tritaniumalloy fragments in Hon-Tihl's body, but also notes that there are severe weapons burns. The Toh'Kaht had been on a bio-survey mission in the Gamma Quadrant, so the final words of Hon'Tihl make little (if any) sense.

Sisko sends Dax and O'Brien out on a runabout to check the wreckage and look for the mission recorder to find out what may have caused the damage. O'Brien promptly gets up to leave, but Dax remains sitting and starts smiling to herself, as if enjoying a private joke. O'Brien calls after her, and she leaves with him for the runabout.

In the meantime, the Valerian ship, Sherval Das, has been trying to get clearance for docking at the station. Kira is trying to keep the Valerians entangled in false delays, but Sisko appears and overrules her. Kira protests by explaining that she did a background check on their ship and has learned that it passed through Fahleena III and Mariah IV, the same two stops that the Valerians made when running dolamide for the Cardassians.

At his bar, Quark is trying to be a good bartender by listening to one of his patrons, but seems to be doing most of the talking. After his patron walks off, Odo arrives and asks Quark what he has heard among the Klingons. Quark complains about the damage the last crew had caused to one of his holosuites, and how they talked of being on a "glorious mission", despite it being a bio-survey. Quark demands a bribe in exchange for more information, but Odo threatens to reassign the work crew away from the holosuite repairs. Quark says that the Klingons mentioned they were in search of something that would "make the enemies of the Klingon Empire tremble." As Odo goes to leave, he screams in agony and grabs his head, which splits in two and collapses in the doorway. A panicked Quark rushes to get Dr. Bashir.

In the infirmary, Odo awakens with a start to find Bashir leaning over him, checking him out. Bashir notes that he had no way of knowing if Odo was all right or not, because his body chemistry defies all of Bashir's instruments. As Odo hastily gets up to leave, Bashir's voice takes on a conniving tone, and he asks if Odo shares his concerns about "the Valerian situation". Confused, Odo asks what he means, and Bashir gloats that the "uneasy alliance" between Sisko and Kira will soon start showing cracks. Odo is put off by Bashir's eerie demeanor and refuses to commit himself to either side of the matter.

Back in Sisko's office, Sisko is busy drawing some sort of blueprint on a PADD when Kira enters. With glee, she announces that the Valerians have visited the Ultima Thule station a week prior, and thus must be carrying dolamide. She announces her intention to board their vessel, confiscate the material, and take them to Bajor to press charges. Sisko, still calm, refuses to allow anything of the sort. Tensions in the room escalate until Kira reminds Sisko that Deep Space 9 is technically Bajoran property. Sisko grimly asks if she is challenging his authority.

On the runabout, Dax and O'Brien locate the debris from the Toh'Kaht. While looking for the mission recorder, O'Brien notes that Kira has been acting aggressively of late, but Dax blows it off as a simple difference of opinion with Sisko. O'Brien does not press the matter, and for a short while the mood of the ship returns to normal. As they sift through the wreckage, O'Brien continues to needle Dax, who seems to be drifting off into her own world. O'Brien cuts off one of her rambling thoughts and demands to know if she's becoming "friendly" with Kira. He advises her to consider her loyalties, and warns that "anyone against Sisko is against me." At this point, they find the mission recorder.

Back in the security office, a seductive Kira enters and starts fawning over Odo, noting that the two of them have worked very well together in the past. Odo responds with caution, and Kira asks for his cooperation in breaking into the Valerian ship to acquire proof of weapons smuggling. Odo asks if Sisko suddenly changed his mind. Kira claims he has. Suspicious, Odo offers to check in with him, prompting Kira to admit her lie. When Odo asks whether she is asking him to go behind Sisko's back, Kira warns him to remember who his friends are, then leaves.

"Personal log, Miles O'Brien. Stardate 46923.1. We've managed to retrieve a portion of the Klingon Officer's journal. Of course, Major Kira heard about it immediately. She must have spies everywhere."

In Ops, O'Brien and Dax present the information they found to Sisko, Kira, and Odo. A recording from Hon'Tihl has been recovered, in which he reveals that he killed the medical officer of the ship, Kee'Bhor, believing that he was a spy from the captain of the ship, Tel'Peh. Through the static, Hon'Tihl can also be heard discussing telepathic energy spheres from Saltah'na, which he suspects are somehow responsible for the violence on the ship. Sisko, obviously bored, flatly states that he doesn't care about anything that happens on a Klingon vessel. O'Brien and Dax continue working on interpolating more of the data in order to fill in the blanks. Dax, still in her own world, childishly remarks that the search is the real reward.

In his bar, Quark set a fancy drink, a modela aperitif, in front of Dax. Kira enters and barks at Quark to "get lost", insulting him and driving him to the other end of the bar. Kira begins to flatter Dax in the same seductive manner she did with Odo earlier. She insists that Dax is the most valuable officer on the station. Dax is oblivious to Kira's advances and continues to quote stories about herself and Sisko. Kira angrily tells Dax that she is going to be rid of Sisko, and threatens Dax with the same. A startled Quark listens to this and accidentally drops a glass. Kira notices Quark's eavesdropping and grabs him by the collar, hoisting him up and throwing him against the back wall of the bar.

Back in Odo's office, Quark enters wearing a neck brace and demands that Odo take action against Kira. He outlines the events in the bar, but Odo is more interested in whether or not Kira managed to persuade Dax. Quark admits that he did not hear much, but that Dax seemed to be "on the fence". Odo inquires about the change in personalities of the other officers, then realizes that Quark hasn't changed at all. With his questions answered, Odo exits, leaving Quark frustrated and demanding satisfaction.

Odo arrives in Sisko's office, but Sisko is nowhere to be found; instead, O'Brien is sitting in Sisko's chair, watching more of Hon'Tihl's journal. O'Brien informs Odo that Sisko is "safe" in his quarters. From the journal, it is noted that Hon'Tihl had placed a thalmerite device near the reactor core to destroy his ship, killing his own crew while he attempted to beam safety to DS9. It seems that there was some sort of mutiny on the ship. O'Brien promises to give Odo access to each of the journal entries as they are reconstructed. On his way out, Odo receives yet another stark warning about his loyalties.

Odo goes to meet with the increasingly reclusive Sisko, and is surprised to find two guards at the door to Sisko's quarters. Inside, Sisko is continuing to work on his blueprints and is becoming apathetic. Odo presents his suspicions about the behavioral changes amongst the crew, but Sisko is uninterested and tells him to go talk to O'Brien. Sisko put down his PADD to reveal that he is drawing up a set of plans for a highly complex clock, which perplexes Odo further.

Odo returns to his office to find Kira relaxing in his chair with her feet on the desk. Kira informs him that she locked down the clamps on the docking pylons to keep the Valerian ship from leaving. She states that she is now going after Sisko and O'Brien, and that she needs Odo's help. Kira entices him with the prospect of a station run entirely by her, where Odo will be given free reign to maintain security however he likes, even to declare martial law. Odo decides to play along and asks what Kira's plan is. However, Kira won't share, knowing that Odo's the most incorruptible person on the station. She prefers to wait until Odo proves his allegiance to her camp. When Kira leaves, a distressed Odo immediately attempts to contact Starfleet Command, but finds that Kira has locked out access. He then tries the Bajoran Council, only to guess that O'Brien has similarly locked them out as well. Fortunately, the computer has finished reconstructing the journal of Hon'Tihl.

In his office, Sisko is busy building his clock while O'Brien paces around impatiently. O'Brien updates Sisko on the situation, and confides his suspicion that Kira is about to make an attempt on Sisko's life. Sisko happily suggests that they should arrest Kira, along with every Bajoran on the station to root all of her sympathizers. O'Brien counsels against it, due to their larger numbers. He instead suggests leaving the station to gather a Federation attack force; at this, Sisko flies into a rage. O'Brien manages to talk Sisko down, but notes that for his plan to work, they will need time to free the Valerian ship so that they can hitch a ride on it.

In the infirmary, Bashir hands a small device to a Bajoran officer and begins telling him how to use it. When Odo enters, both react as if caught, but Bashir pretends to be giving the Bajoran medical advice. The Bajoran leaves, and Bashir smugly advises Odo to choose sides soon, as events have moved swiftly since their last conversation. Odo decides to talk to Bashir as if he were a co-conspirator, in order to coerce information about the Klingon first officer's autopsy out of him. It seems that there were some symptoms that could have arisen due to some sort of telepathic influence, and that the telepathic archives from the energy spheres could be reenacting the power struggle that had destroyed the Saltah'nan civilization. The only people who have been affected were standing in Ops when Hon'Tihl beamed on board. Odo theorizes that the anomaly tried to control him too, but that he was unaffected due to his lack of a humanoid brain; this explains his earlier seizure in Quark's Bar. Odo coerces Bashir into helping to find a way of removing the telepathic influence, promising him that the means to remove the virus is the key to seizing control of the station for themselves. This nullifies Bashir's suspicion and makes him cooperative.

Back in Ops, O'Brien is still laboring to release the docking clamps, with Dax's help. Sisko steps out of his office to see how much progress is being made. The Bajoran officer that was in the infirmary earlier exchanges a glance with Dax, then takes a PADD over to Sisko. In a flash, he pulls out the device that Bashir gave him and prepares to jab it into Sisko's back, but O'Brien sees it and alerts Sisko. Dax instantly contacts Kira, revealing herself to be a conspirator; O'Brien hits her across the face and silences her. Sisko violently interrogates the Bajoran as to whether or not Kira put him up to this. He picks up the weapon the Bajoran dropped and prepares to use it on him, but at that moment Kira and her guards storm into Ops. Kira points a phaser at Sisko, telling him to drop the device.

Kira commands her group to seize O'Brien and Sisko. O'Brien cautiously reaches his hand to the control panel, and both he and Sisko beam out of the room. Frustrated, Kira demands to know why Dax didn't disable the transporters, to which Dax groggily replies "I forgot..."

In an airlock corridor, O'Brien and Sisko find that instead of materializing on board the Valerian ship, their transporter signal has been diverted by Kira, and they are now blocked in on both sides by force fields. Despite his apprehension as to Odo's loyalty, Sisko contacts him for help. Odo uses his priority security codes to guide the pair to the cargo bay entrance at docking bay 4. After the call, both O'Brien and Sisko leave their combadges behind, so that their movements won't be traced.

Meanwhile, back at Ops, Kira and Dax are confused as to why Sisko and O'Brien don't appear to be moving, before realizing that they must have discarded their combadges. Kira quickly deduces that someone has been overriding their security force fields. In anger, she contacts Odo and demands to know what side he is on. Odo coolly replies that he is with her, and that he has just trapped Sisko and O'Brien behind the impenetrable cargo bay door. Bashir, still conspiring with Odo, expresses admiration at Odo's ploy and announces that he has set up an interference signal in that cargo bay, to drive the telepathic field out of the afflicted officers.

In the cargo bay, Sisko and O'Brien discover that they are trapped. Kira, Dax, and their guards make their appearance at the opposite end of the bay. Sisko admonishes Kira for her lack of gratitude, and declares that history will vindicate him. Just as Kira is about to kill Sisko, Odo and Bashir open the door that O'Brien has been trying to open. Odo tells the computer to execute his program, and a strange wave of energy passes through the air of the room. Everyone drops their weapons and, save for Odo, collapses in pain as the telepathic force is driven from their minds. Odo advises everyone to grab onto something, then opens the airlock. The energy field is sucked out of the station into space, and Odo triggers the door shut again.

"Commander's log, stardate 46924.5. With nothing to contain it, the telepathic matrix has dispersed in space. Meanwhile I'm happy to report everything and everyone aboard DS9 has returned to normal."

In the commander's office, Sisko and Kira discuss the strange clock that Sisko built during his affliction. Kira expresses deep regret for her attempted mutiny. Sisko replies "I think we'll let it go... this time." Sisko then focuses his attention on the clock, starts it and seems to still be fascinated by it.

"I've been friends with Benjamin Sisko for many years... In many ways, he's like a son. Or a nephew... Some kind of close relative anyway..."

- Jadzia Dax

"Is this a Ferengi fashion I'm not aware of?"

- Odo, after Quark enters his office wearing a neck brace

"How are you, Lieutenant?"
(tired)"You know what they say – put the shoe on the right foot first, but put the left foot first into the bathtub."
(confused) "I understand."

- Kira and Dax

"What do you think?"
"What is it?"
"A clock! Fascinating, isn't it?"

- Sisko and Odo, as Sisko shows off his handiwork

"Anyone who's against Sisko is against me."

- O'Brien

"The Klingon, Doctor; what did you find?"
"He's still dead, if that's what you mean."

- Odo and Bashir

"I want you to arrest them. Kira and every Bajoran officer on this station. I want the names of every sympathizer..."
"That's not a good idea, sir. There are a lot more of them than there are of us. If we tip our hand, it could work against us."
"What can we do?"
"Leave the station."
(shouting) "NEVER! Get me a phaser, and I'll get rid of Kira!"
"Hear me out, sir... We leave the station. Raise a Federation attack force... and return. (pause) And on that day we'll get rid of all your enemies."
"How do we proceed?"
"I need a few more hours to free up the Valerian ship. I've already talked to their captain. He's more than happy to take us back to Federation space."
(whispering) "Call me as soon as you're ready."

- Sisko and O'Brien

"So, this is how it all ends."
"For you."
"You know what disturbs me? The ingratitude. I offered you my kindness, my help, my leadership and how do you repay me? With betrayal. But you won't get rid of me so easily. You see, unlike you, I understand history. My name will blaze across the stars long after your petty treacheries have been forgotten."
"But you won't be here to see it."

Of his original concept for this show, writer Joe Menosky says, "I wondered if there could be something like a telepathic virus, a little packet of telepathic energy containing something that works in the same way that a virus co-opts the genetic code of a living cell and then changes its biology according to its own design. This would do the same thing, but according to a kind of theatrical complex that it carried, transmit a little drama. Each one of these telepathic viruses represents a little play, containing a bunch of character dramatics and emotions and traumas that had happened. In this particular case, the little play was a power struggle that led to the fall of a race or a civilization." (Star Trek: Deep Space Nine Companion)

This episode is a favorite of Ira Steven Behr, who feels it was a bold move to do a show like this so early in the series; "it was a third season show that we had the nerve to do in the first season. Anybody else would say 'You need to know the characters better before you twist them like this.' But seeing Kira come on to Dax – I don't care if it's first or third season, people are going to be interested in that!" (Star Trek: Deep Space Nine Companion)

Bole was also pleased with the performances of Rene Auberjonois and Armin Shimerman, noting that "We had a marvelous scene with Armin, when Quark and Odo were together. It's kind of the way I remember Charles Laughton and Peter Ustinov when I was doing script work on Spartacus. The screen just lit up when they were working together, and that's what happens with these two guys, they're marvelous". (Captains' Logs Supplemental - The Unauthorized Guide to the New Trek Voyages, p 55)

Armin Shimerman was very pleased with how the episode turned out and the context behind it, commenting "I loved this episode. I love the fact that revolution broke out. Even though it wasn't a real revolution, I still love the conflict between Sisko and Kira, a person who is a national and who only thinks of her world first. I love those issues of nationalism because we go through that here in Los Angeles a lot. We had our riots because neighbourhoods felt that they weren't getting a fair share of the wealth of Los Angeles, and there's the Bajorans who are fighting because they're not getting a fair share of what they think they deserve. That's very intrinsic to the life we live in Los Angeles, so when it's represented on television, I feel for that". (Captains' Logs Supplemental - The Unauthorized Guide to the New Trek Voyages, p 55)